Fall of Pegasus
by Imperial Bob
Summary: An ancient portal is opened, unleashing the horrors of the 41st Millennium in the naive stargate universe.What will become of the galaxy embroiled in a new war between ancients and the hungering horde? Includes Daniel and Vala! Yaay!
1. Chapter 1

From the armored bridge of the battleship, Captain Augustine looked over the system. The fleet was positioned strategically around the cogboys encampment on one of the dull, brown misshaped asteroids. The captain observed the colorful asteroid belt, constituted of purple and blue gases. It was quite a sight to behold, yet the captain wouldn't let such trivial things as beauty distract him. He had been given a specific task, after all.

On the asteroid, the AdMech were busy toiling away at the thick rock, eager to reveal more of the strange ruins; large mining and excavation servitors drilling endlessly. The initial ruins were uncovered by a mining team. During their prospecting they had accessed a queer corridor; its smooth black walls a stark juxtaposition against the dirty dull brown. This was most perturbing to the Adeptus Mechanicus, as the entire system had been sealed off by a warpstorm for millennia. Whoever had constructed the ruins must have been here since before the rise of the Imperium of Man, which in and of it's self was nothing significant. Millions of species had risen and fell since the dawn of time.

"Commander," someone had entered the captains annex, it was Augustine's aide, Jarkin, who now stood in his portal-way. "We've received a message from Parthia, sir, it's a distress call."

"A distress call?" the commander responded, not breaking his gaze from the viewport.

"Yes sir," his aide stuttered, "They've been hit by Eldar raiders,"

"Hmm, unfortunate. Relay the call to the nearest Navy garrison."

"But sir, surely we could break anchor and-"

"You heard me Jarkin. I'm not here to hunt for glory; I'm here on orders to take care of these here cogboys." The Captain said, gesturing to the rock. He didn't need to say anything further; Jarkin knew he was alluding to Captain Morilda. She had been stationed in orbit around some backwater agri-world when she decided to break orders and assail a local ork rokk that had just exited warpspace. Short to say, the world was lost to the forces of Chaos, and the supposed ork rokk was nothing more than a lifeless space hulk. In the time it took her to reach it, the world had already fallen. Such a recent failure remained pertinent in the crew's mind. Shame too, she had a pretty good record.

On the planet progress was progressing smoothly, the local Explorator in charge, a techpriest by the name of Dalvon, was supervising the effort to unearth the ruins. All around him his entourage manned various Auspexes and other more complicated sensor equipment that the sergeant couldn't identify. He had been billeted with the techpriests to keep the captain in the loop

"Are you sure it's safe?" He asked.

"Of course," the techpriest said in a condescending, grating voice, "It hasn't been inhabited for thousands of years." His augmentic eye whirring as it refocused on the sergeant. Most of this face had been remade with augmentics, and the sarge found it hard to focus on the squirming mechandrites and data-plugs he had in place of a mouth, the Vox unit that he had spoken from lodged where his Adams-apple should have been.

The Sergeant sighed. He'd never know why the commander saw him the most likely candidate for the job. Quite frankly, he found cogboys awkward at the best of times, and disturbing and unholy at others. He'd always been taught in the schola, "to pollute the human form is heresy". "Uncouth bastard," he muttered under his breath. _Shit, _he thought, _I hope he doesn't have hearing augments._

As if on queue, the entire asteroid resounded.

"What the khek was that?" the sergeant demanded

"The ruins are giving off a massive energy reading!" The techpriest said, and given the situation the Sergeant resisted an "I told you so". Eerily, the black walls became disgusting, as if they were an affront to the sergeants most base and primal instincts. _Are… are the walls glowing... _

"Sire, I have an interesting reading," announced one of the techpriests manning a work station in the bridge. "It appears to be eldar in origin, they've exited warp."

"Eldar?" the captain asked, "What in the warp are they doing here?" He shook such thoughts from his head, _it matters not why they are here; they will die anyways._ "Wake the crew! I want those ships targeted, if a lock cannot be maintained I want fire evenly dispersed!" He never did like squaring off against eldar, it was like striking at vague shadows.

The bridge picked up in pace as the techpriests and helmsmen hurried to turn the captains words into actions. All around the ship serfs sprung to action. The men manned their stations supervising them, ensuring none broke rank, and they began loading the massive macro-cannons and preparing the weapons. Techpriests initiated rites, the entire ship was alive, and the captain's orders willing it to action like the head of some massive carnivorous beast.

"Targets acquired, lord,"

"Fire!" In an intense moment space was brightened from the light from the breeches of the guns. The devilishly sleek and maneuverable eldar ships easily avoiding the thickest of fire, aided by their dancing holo-fields. The eldar returned fire and pulsars and plasma splashed against the Imperial battleship's void shields.

In moments, the lone battleship was aided by 5 escorts that had been in a loose picket around the asteroid, adding their firepower into the fray. In the crossfire one eldar craft was caught and torn asunder, its shields failing under such torrential assault, its hull buckling before the entire ship went up in a massive plasma explosion.

Suddenly, the ships jeered, performing acrobatics that Imperial captains could only dream of, their course changed, they began heading straight for the asteroid. "Stop those ships!" Augustine ordered, "Don't let them interrupt the Mechanicus' work!" The eldar craft continued their course, when suddenly they overlapped with the asteroid, to the captain's horror. "Cease fire! Cease fire immediately!" he roared, yet it was too late, the damage was done.

A full broadside was unleashed, and while it caught at least two eldar craft in its wake, the rest of the massive shells overshot and slammed into the asteroid. Under such an assault, it snapped into several pieces, secondary explosions rippling throughout the catacombs from the AdMech's tunnels and the ruins.

The entire asteroid shook again, and the entire interior of it was filled with the sounds of collision, bending metal and ear-rending explosions. The sergeant was silent, all color drained from his face. The walls had changed, somehow. Despite the happenings around him he was entranced by the walls, the smooth black walls. The techpriest was busy pouring over his equipment, issuing orders to his underlings in the gibberish, clicking speech of his order.

Yes, yes the sergeant was sure of it now. The walls were illuminated, bathed in a green glow. The techpriest confirmed this, "The ruins are active! The energy readings are off of the chart!"

And then, staring at the walls, the sergeant was bathed in flame. It was a more placid death then he probably deserved.

The entire asteroid at this point had been shredded into too many pieces to count; the largest remaining body was the chunk of rock the ruins were embedded in, now glowing an eerie green.

"The ruins are unstable, the readings are growing!" the techpriest shouted on the bridge of _Imperator's Deliverant_, before the ruins exploded into a ball of malevolent, rippling green waves, washing over the eldar and imperials without prejudice.

* * *

><p><strong>In the Pegasus galaxy;<strong>

Doctor Elizabeth Weir looked over the calm blue waters of Lantea, stretching to the far horizon. Before, back on Earth, when the president contacted her, she had no idea it would land her here, far away from home in the Pegasus galaxy. She let out a tentative sigh. It was stressful at the best of times, but she wouldn't give this chance to explore the unknown for anything in either two galaxies.

"Doctor Weir," someone announced over the intercom, "Scheduled activation's coming up from Stargate command."

"Right, thank you," _How could I forget! _She thought.

In the gate room Colonel Shepard and his team were already standing at the ready for the incoming wormhole. The gate spun and the chevrons locked, enveloping the room in the blue glow of the rippling portal. First to step out of the portal was Doctor Daniel Jackson, carrying a rucksack over his shoulder as he walked down the dais. The next and last person to arrive was Vala Mal Doran, her pigtails resting on her shoulders. She also carried a rucksack to her side in her right hand.

"Doctor Jackson," Weir welcomed, "And Vala. Good to see you."

"And you two, Doctor Weir," breezily replied Daniel, "I hate to be curt, but I'd like to start working as soon as possible."

"Right," Weir said, a bit taken aback. She didn't expect them to be in such a hurry. "The information you've requested has already been gathered and is waiting for you." She gestured to the corridor leading to the room she had prepared for them.

"Thank you," Daniel replied, moving past her into the corridor, followed by Vala.

"He's a workaholic," she said as she passed Weir without breaking stride, however giving her the courtesy to face her direction by walking backwards, before hurrying to catch up to Daniel.

"Not even a hello?" Rodney chimed; a plaintive look on his face.

"What's wrong Rodney? Thought she'd remember you?" Ronnon teased.

"What—no it's nothing like that. I thought Daniel would remember the work we did together, that one time," he trailed off in his own thoughts.

"I didn't know you rolled both ways," Shepard joined in on the teasing.

"Oh hah-hah very funny guys." Rodney finished, following the rest of the team out. They were only there for procedure, although frankly they all expected a much warmer welcome.

Several hours later, in the same gate room AR-1 waited in full kit, carrying their signature P-90s.

"Alright, this is just a standard recon mission. The current planet is believed to have a few sleeping wraithships, so watch your backs. Latest reports still list them as inactive though, strangely." Weir told the team in person, "I expect you back in one piece, Colonel, no brave heroics, got it?"

"Yes ma'am." The colonel replied. He remembered with a shudder what happened the last time they had infiltrated a hive.

With a _whirr_ and a _whoosh_ the stargate opened up, and AR-1 was away.

The planet was comfortable enough, warm clime, easy topography and a beautiful beach line not to far from the pedestal the stargate rested on. Stretching from the coast to the thick foliage were small buildings and markets, were people busily went about their day. Their was something in the air though, as people skittered around.

When they reached the township they introduced themselves, the previous Atlantis team dispatched had already taken care of most of the formalities.

"How do you do," Shepard asked a man in rags and leather working a fruit stall.

"G-good," He stuttered, "You're from Atlantis?" He asked, looking at Shepard and his team's vestments and weapons.

"Yes," replied Tayla, "We mean you no harm." She added in when she saw his cursory glances.

"R-right,"

"What's wrong?"

"Nothing is wrong!" he practically yelled, raising concerned glances among the team. "I think he's crazy," Rodney silently said. "That's the thing!" the man continued, "The wraith, the wraith are gone!"

"The wraith are gone?" Asked Ronnon

"Yes! Two days ago, fire rained from the sky, and the avenging angels came! The wraith, they were just swept away…" he trailed off. Shepard seemed to get now what was in the air, anxiety. Something more powerful than the wraith had come, and disappeared.

From there the team went off along some roughly hewn dirt road.

"What do you think it was?" Asked Rodney, a concerned look plastered on his face. Undoubtedly he was only concerned for his skin.

"Ancients?" proposed Ronnon.

"People around the village spoke of ghosts and shadows," Tayla added, "Even if they were Atlaneteans, in doesn't fit. The Atlanteans always fought with pride and honor, championing themselves. Why would they cower?"

The team broke off at a certain point, into the dense foliage. On the other side was a sight that startled them. The wraithship the previous team had found in the clearing was shattered, now nothing more than a smoldering husk, the fires long dying out to smolders. All around lied wraith bodies, torn and dissected. It looked less like a space faring race and come, and more like a ravenous horde.

"Holy crap," Rodney was first to break the silence.

"Alright, I think it's time we reported back to the good Doctor," Shepard said, taking quick stock of the situation. He never would have expected this from a standard recon mission.

Back at the Stargate, the team contacted Atlantis.

"Shepard? I wasn't expecting to hear from you so soon," she started

"Well things here have changed, boss."

"What do you mean 'things'?"

"The wraith are dead. I'd like a medical team out here to help collect some bodies."

"Right away," she said, motioning off screen to people outside of view.

"And tell Jackson that we have something he may like to take a look at."


	2. Chapter 2: Ruins

The gate roared open once again. First to step out this time was Vala, wearing a wide brimmed sun hat and a smile. Doctor Jackson was next, however he wasn't in such a jolly mood. With him he carried a kit that surely held the tools of his trade. He was clearly in the middle of a sentence before entering the gate, and he fnished it after being resembled on the other side of the gate. "—ean I don't know what they expect we'll find."

"Oh, cheer up Daniel!" Vala told him, enjoying the sun and brisk breeze. The sky was bluer than the Lantean one, with twin suns in the sky, giving off an orange glow and warming the planet's poles to tropical levels. The temperate town they were currently in was actually quite close to the equator.

"Doctor Jackson, Vala," greeted Shepard, and last to arrive was Doctor Carson. "Bloody hell," he said, stepping out of the gate. He wasn't used to gate-travel yet. "And Doctor Carson, right. Well town's this way." He said, gesturing and down the beaten dirt path roughly hewn through a motley collection of palm trees to the visible downhill residency.

The town was rather small and humble to the collected Earthers, yet still excreted a sense of warm cozy, comfort with its sandstone buildings along the shore and what looked like palm trees. On the peripheral of the town were small yet cozy looking homes and manors, with denser and taller, terraced buildings becoming thicker the closer you went to the center of the town. Potted plants hung, and people waded through the tide of persons in the bustling tight alleyways of the city center, while vendors and people took on a much more relaxed pace on the outskirts.

At least Vala seemed to appreciate it, Daniel looked disappointed to have been pulled from his work. For all he knew the ruins could simply be from the last culling, and not the mighty Lanteans. He had decided it was worth a look however. The Milky Way could use every advantage it could get over the Ori, and if this short voyage uncovered anything Lantean then it would be worth the time. He just hoped there weren't any spiders on this planet.

Once in the outskirts of the town, Teyla went off with Ronnon to find a guide to the ruins. The rest of the team stayed behind, lounging in the tavern's outdoor iron wrought chairs. Shepard remained standing. "Well Daniel?" Vala asked, "Glad you left that cramped little room?"

"No," he said, "Would be better if we had left you behind," he teased, or at least that's how Vala decided to interpret it.

A barmaid came out with a platter of water mugs and offered them to the team. "No thank you," Rodney rejected. "Do you know what could be in this water?" he asked the rest of the team that took the offer.

"Cool deliciousness?" Vala answered his question with a question before sipping her drink.

"Well that, and horrible bacteria,"

"Bacteria?" Asked the Barmaid, "Those like ghosts? We've had plenty of those around 'ere lately,"

"Ghosts?" Asked Shepard

"Aye, ghosts, we been hearin' reports of 'em 'ight after those wraith were kilt, 'specially 'round des ruins."

"Well that's just perfect," commented Rodney.

Teyla and Ronnon returned with a guide from the village. He was short and stout, clothed in leather with a cowl, but he claimed to know the way and was willing to take the team there. No one else had dared venture to the ruins since the rumors started, and even before that people generally stayed away from them. He had agreed to take them there in exchange for some coinage they used on the planet, which wasn't that hard to attain thanks to Vala, although Teyla disapproved.

First, the team stopped by the clearing. "What's here," asked Vala.

"The clearing we mentioned, Doc,"

"Oh right," Carson began moving, readying his field equipment he carried with him in his duffel-bag. The carnage was still there when they arrived, undisturbed by the locals or even carrion birds. The fires had died out by now. "Let's see..." started Carson, kneeling by some bodies. "I'd like to take some back with us to Atlantis." He began prodding some of the dead wraith with a stick.

"Best wait awhile Doc, I think Daniel will like to take a while to look at the ruins," Shepard said, grinning at Daniel

"Well, we don't know about that yet, Shepard" Daniel replied. Vala gave a pouty face, her expression worth a thousand words, "Don't make me go back to that little room with you."

* * *

><p>"These ruins are amazing!" Daniel Jackson said excitedly. He had been analyzing the Ancient ruins now for at least an hour. They had yet to even begin to explore the caves. The ruins were for the most part fallen columns, overgrown tiles and tablets etched into the stone wall outside the cave entrances, which Daniel found the most interesting. "According to these writings, these caves link up to an Ancient outpost, like the one found in Antarctica. Don't know what they were used for though, possibly defense. Although the way they're mentioned here makes it seem more like a research outpost. I mean, who knows what we can find down there, we may even find something to help us combat the Ori-"<p>

"Right, glad to see you're having fun Daniel," Vala blurted cutting him off, clearly bored out of her mind, long since giving up on pestering him while he worked. She was reclining on a nearby boulder, arms crossed behind her head, watching the clouds.

"Well, I'm going to go check on the doc. See what he's found for us," Shepard announced gesturing towards the clearing they'd found the burnt out wraithship, glad to be leaving Daniel and Vala to their own devices. He liked the young doctor and the... cheeky rascal? but he could use a break to check his sanity.

"Aye, Shepard," he greeted as he cleared his throat. "Thought you were a ghost," he chuckled. "Don't sneak up on me like that,"

"Well doc, what can you tell me?" he asked the doctor, currently kneeling beside a wraith he had been analyzing. Shepard could see the wraith had been neatly bisected into two halves from his right shoulder to his left hip. It was definitely too neat for some feral animal, yet to brutal to have been done by the hands of a human in one fell swoop. The wraith looked as if they had been dispatched in multiply ways, all of them bloody and rather personal.

"Well, not much sadly. Although, these wraith died in a cruel number of ways. For example this one, was torn apart by mini-rockets it seems. And then this one over 'ere," he said, gesturing, "was sliced clean in half. Was probably from a sword."

"A sword?" Shepard asked.

"Yes, I've found plenty of vertical striations that point to long bladed instruments. Swords, colonel. A knife sure couldn't have done this" He said gesturing to the bisected corpse he was kneeling next too.

"Right, great. So we're facing sword wielding ninjas."

"Well, that's not all. I've also found these pointy star thingies, embedded in the ground. Looks like they went right through the wraith themselves, I mean in order to do that you'd have to propel them to extraordinarily fast speeds"

"... shurikens?" Things just kept on getting weirder and weirder. "Doc, did you see that?" He asked, noticing a bush move out of the corner of his eye, drawing his holstered pistol in one smooth motion.

"See what?"

"Was probably nothing." _Damn jitters, all this talk of ghosts, _he thought, _you're a colonel dammit! Quit acting like a frightened 10 year old and act like it. _

"Hey, Shepard," Vala rang over the radio, "Daniel's found something,"

* * *

><p>She was right. When Shepard returned to the mouth of the caves he saw what she meant. Hidden behind some foliage was a large, curved column like edifice rising from a base. <em>How did we miss that? <em>He thought. The thing was easily 9 feet tall, even behind the brush he couldn't imagine how something like that could remain hidden for so long. It was a weird structure, unlike the flat gray Lantean ones, it was an off white, with black detailing and dark red gemstones. Daniel was busy copying the symbols at the base into his notebook, while Vala watched from behind him.

"What is it?" he asked upon arriving.

"I don't know," Daniel responded, "It's not Ancient, the writing doesn't match anything we've come across before either,"

Vala eyed their surroundings. She had a bad feeling. Probably why most people stayed away from the area. However, she trusted her intuition, as it had gotten her through some very tough obstacles and out of some very tight pinches. And now she felt like she was being watched. "I also want to explore the caves," Daniel announced.

"Well it's about time, Rodney! Teyla! Ronnon! Come on, we're going down into the caves,"

"What? Now? Shouldn't we bring another team to watch our backs or something?" Asked Rodney,

"Watch our backs from what?" countered Ronnon

"Ghosts?" Shepard teased, remembering his over reaction earlier. "Come on, the sooner we're done the sooner we can get back home."

The entrance to the cave was natural enough, rough brown dirt and grey stone gently descending into the sheer face. In places there were alcoves and tablets etched into the walls in Ancient, and broken tiled floors. The cave's roof was plenty high, leaving Rodney feeling rather secure and comfortable with the airy passageways. After a dozen or so minutes they finally reached the outpost. Big blocky doors marred their entrance, with a crystal door control set into the neighboring wall.

"Give me a minute," Rodney hooked his tablet up to the door controls. After a few magical button presses the door slide open. "Ah, there we go."

The room was pitch black and musty, and probably hadn't been opened in ages. Shepard coughed as he inhaled the collected debris and dust bunnies in the air that was stirred up by the door. The rest of the team pulled up their shirts to protect their nostrils and turned on their flash-lights attached to their collective P-90s.

"I'm sure there must be a light switch somewhere," chimed Vala.

"Well of course, I find it hard to believe they did their work in the dark," Rodney commented, "Sorry, right." He eventually found it after feeling around on the wall. The dust had also settled, alowing the team to pull their collars down.

The lights revealed a rather large room, with consoles clustered around and vials of a green, bubbly liquid in the walls. The lights were an eerie dull off white that flickered sporadically. Rodney theorized it was from the lack of maintenance. The roof here was higher than the passageways, and the open passages revealed the lowered ceilings.

"Alright, split up. Stay in radio contact, remember we're not going to stay long. Just take a look around."

The team split into two, the first with Shepard, Daniel and Vala and the second with Teyla, Ronnon and Rodney. The outpost was rather large, with winding poorly lit cramped corridors the deeper you went, with half walls and see through glass. So far most of it seemed rather normal and abandoned, if a bit off-putting.

* * *

><p>It was when Rodney opened one of the deeper doors did things seem amiss. The door slid open reluctantly, and an unpleasant smell wafted through. "Ugh, what is that." Asked Ronnon.<p>

"Let's find out," answered Teyla, shouldering her P-90. The lightning here was a dull green, with tubes full of the green liquid lining both sides of the wall giving off a kind of bio-luminescence.

"Oh god," Rodney simply said. Old blood stained the walls and floors, consoles covered like they were painted red. There were no skeletons or bodies, but what was found in the vats was even more disconcerting than the aged carnage laying on the room's surfaces. Their bodies silhouetted by the glowing fluid, the team couldn't get a very good look at any one in particular, however their very shape just held a wrongness. Some were humanoid in shape, except they had exaggerated features, like arms, or shrunken features. Some even had extra limbs and protrusions that looked like tails, or claws, or tentacles. "What the hell are those?" He said stepping back.

* * *

><p>In another part of the installation Daniel Jackson was busy studying a research console, making sure to take notes of it and the information it held. Vala hung behind him at another console. The thing was studded with runes and buttons, just begging to be pushed...<p>

* * *

><p>With a hermetic hiss the vats began to drain, and the tubes began to lower. Teyla and Ronnon instantly brought up their weapons. "Crap, power readings just went up!" Rodney said, rabidly checking and working on his tablet. The things inside slowly became animate, and the team backed out the door from which they came. Rodney was already trying to seal the door, "It won't budge!"<p>

The first thing out was truly a hideous sight to behold, with a malformed mouth, with fibers holding it together in pieces, and it's entire rest of it's face looked squished together, it's flesh looked as if it had been partially melted off. It's right arm wasn't an arm at all but rather an over-sized claw, and it looked like it a devil of yore with three deformed horns poking out from under it's scalp. It's mouth produced a horrifying screech, before it charged.

Teyla was the fastest to react, filling the hellish creature with hot lead. The thing was nearly bisected and yet it kept on coming until Ronnon managed to add his firepower, his pistol blasts finally bringing it down, only for three more creatures to leave their vats, each as uniquely deformed as the first. One with an oversized mouth bellowed a howl before charging, it's hoof feet leading the way before it was dropped by Teyla's and Ronnon's combined firepower. The next one was able to get closer as Teyla had to reload. Ronnon's blast however seemed to keep it back long enough enough for Rodney to finally seal the door. The creature slammed into it, and judging from the sounds, began to flail against it, howling. "Now would be a very good time to be leaving!"

The team ran the way back to the main vaulted atrium, sealing every door they came across. Some open rooms they passed still held occupants in the vats, and others to their horror were empty, wet footprints leading the way out for a while only to disappear.

By the time they reached the way they entered they were all breathless.

"What the hell happened to you?" Shepard asked

"We, gotta get out of here," Rodney managed to say between ragged breaths, "Things, vats, leave now."

They made sure to seal the main doors. Deep in the complex, unannounced to them, a deep war cry of "WAAAAAGH!" resounded through the cramped rooms and corridors.


End file.
